Topic 3.8: Photosynthesis

3.8.1 State that photosynthesis involves conversion of light energy into chemical energy.

Photosynthesis is the process by which plants synthesis organic compounds (e.g glucose) from inorganic compounds (carbon dioxide and oxygen) in the presence of sunlight

3.8.2 State that light from the Sun is composed of a range of wavelengths (colours).

Light from the sunlight is made up of all the colours of the electro-magnetic spectrum

3.8.3 State that chlorophyll is the main photosynthetic pigment

Chlorophyll is the main site of light absorption in the light dependent stage of photosynthesis. There are a different number of chlorophyll molecule, each with their own distinct absorption spectra.

3.8.4 Outline the differences in absorption of red, blue and green light by the chlorophyll

This is a graph that shows the light absorption spectra

The main colour of light that is absorbed are red and blue. Green is the colour that is mainly reflected. Thus the green colour we can see from the chloroplast. During the winter times, trees produce less chlorophyll as there are less sunlight. Thus the change in colour of leaves during the different season

3.8.5 State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen.

Photosynthesis consists of two reactions; light dependent and light independent.

Light Dependent

• Light is absorbed by the chlorophyll molecules (green) inside the chloroplast
• The light energy from the photons (light) is transferred to excite the electrons thus changing the energy from light to chemical
• The chemical energy is used to produce ATP

• Light energy also splits the water molecule in a process called photolysis, producing oxygen and hydrogen
• The hydrogen is taken up by the hydrogen carrier (NADP+) to form NADPH
• The splitting of water also releases electrons which replaces the loss of electrons in the chloroplast
• The products of these two reaction are then taken to the light independent reaction

3.8.6 State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules.

The second part of photosynthesis uses the products from the light dependent reaction

• ATP and hydrogen carriers are the products of the light dependent reaction
• They are used to fix the carbon molecules together, adding carbon dioxide to an organic compound.
• This allows for more complex organic molecules (e.g. sugars)
• The organic molecules are then used in cellular respiration or stored as starch.

3.8.7 Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass

The rate of photosynthesis can be measured by the production of oxygen, the uptake of carbon dioxide or the increase in biomass. But water can't be used as a measure because it is also used in other process.

Measuring carbon dioxide uptake

• Carbon dioxide uptake can be measured by placing a plant in an enclosed space with water
• Carbon dioxide interacts with the water molecules, producing bicarbonate and hydrogen ions. This increases the acidity of the solution
• The change in pH can be used to measure the uptake by a plant (More carbon dioxide =  More alkaline solution)

Measuring oxygen production

• Oxygen production can be measure by submerging a plant in an enclosed space with water attached to a sealed gas syringe
• Any production of water will change the meniscus of the sealed gas syringe

Measuring change in biomass

• To measure glucose production, the change of biomass could be measured
• The plant is required to be completely dehydrated to ensure the change in biomass reflects a change in organic matter and not water intake.
• Or measure the change in starch content in a plant. This could be quantitative data by using a colorimeter.

3.8.8 Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.

Rate of photosynthesis:

Photosynthesis is a biological reaction which also requires the assistance of enzymes. Temperature will increase the rate of reaction by increasing the chances of reaction happening. However, once it reaches (c), the enzymes will denature and the reaction will no longer be able to take place.

The effect of carbon dioxide concentration on the rate of photosynthesis. As carbon dioxide is one of the reactants in the reaction, an increase of concentration will increase the probability of the reaction taking place. However the curve will converge as there will be another limiting factor.

Light is an important element required in photosynthesis. An increase in the light intensity will increase the rate of reaction. However the curve will start to converge as there will be a limiting factor which stops the rate of reaction from increasing.

Topic 3.7: Cell respiration

3.7.1 Define cell respiration

Cell respiration is the controlled release of energy from organic compounds in cells to form ATP.

3.7.2 State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP

Glucose is the breakdown of one molecule of glucose (6 carbon) into two molecules of pyruvate (2 x 3 carbon) with a small yield of ATP.

This is the whole process. Further discussed in HL.


3.7.3 Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP

Anaerobic respiration occurs in the absence of oxygen.

In order to generate small amount of energy and the two NADH, the electrons are transferred to the pyruvic acid to form lactate.

In the plants (yeast), the final product that is produced is Ethanol with is a simple 2 carbon substance and carbon dioxide per pyruvate molecule.


3.7.4 Explain that, during aerobic cell respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP

In the mitochondrion, the pyruvate molecule then processes through the Kreb's cycle and electron transport chain to produce water and carbon dioxide with 34-36 ATP molecules.

Although before this process is glycolysis, it is adviced to remember that oxygen was not used in glycolysis.

This is the final table of the whole process

Topic 3.6: Enzymes

3.6.1 Define enzymes and active site

What is an enzyme?

• An enzyme is a globular protein that increases the rate of reaction by lowering the activational energy threshold
• It is also known as the biological catalyst

Active site is the position on the enzyme that is occupied by the substrate.

3.6.2 Explain enzyme-substrate specificity

• Enzyme and substrate are complements of each other in terms of shape and chemical properties
• Binding to active site brings the substrate into close physical proximity, creating an enzyme-substrate complex
• The enzyme catalyst the conversion of the substrate into a product, thus changing into an enzyme-product complex
• As the enzyme is not consumed during the reaction, it can continue with another substrate.
• Note: Reaction can go both ways. 

Lock & Key hypothesis states that one key to one lock. Thus one enzyme to one particular substrate. The enzymes specificity is due to the complementary shape of the active site and the substrate.

3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity.

Temperature

• Low energy results in insufficient energy for the reaction to take place
• Increasing the temperature will increase the kinetic energy of the substrate and enzyme, thus increasing the chances of collision.
• There is an optimal temperature at which the enzyme could work
• When the temperature is too high, the hydrogen bonds in the enzyme breaks and the enzyme loses its shape thus changing the active site.

pH

• Changing the pH could alter the charge of the enzyme.
• Thus causing a change in shape and changing the active site.
• Enzymes have an optimal pH.

Substrate concentration

• Increasing substrate concentration will increase the chances of collision
• After a certain point, the environment will be too saturated with substrate that the enzymes can't react any faster.

3.6.4 Define denaturation

Denaturation is the structural change in the protein that results in the loss of its biological and chemical properties.

3.6.5 Explain the use of lactase in the production of lactose-free milk

Lactose is a disaccharide (Glucose + Ga(lactose)), while lactase is the enzyme that breaks lactose down.

As majority of the human population are somewhat lactose intolerant, the milk industry needs to produce lactose-free milk.

Milk is repeated passed through this process to ensure lactose-free. As enzymes could be easily re-used, this is a cheap and efficient process.

Topic 3.5: Transcription and translation

3.5.1 Compare the structure of RNA and DNA

3.5.2 Outline DNA transcription in terms of formation of an RNA strand complementary to the DNA strand by RNA polymerase

The DNA transcription process aims to create mRNA (messenger RNA - carries the codons).

• The DNA helix is unwound using RNA polymerase at the position of the gene
• RNA ribonucleotides triphosphate aligns with their complementary pairs. (Uracil replaces Thymine)
• Once RNA polmerase has full synthesized, the RNA polymerase will detach itself form the DNA molecule and the double helix will reform
• Transcription occurs in the nucleus.

3.5.3 Describe the genetic code in terms of codons composed of triplets of bases.

The genetic code is the set of rules by which information encoded in mRNA sequences is converted into proteins (amino acids sequences) by living cells

• Codons are a triplet of bases which encodes a particular amino acid
• As there are four bases, there are 64 different codon combinations 
• The order of the codon determines the amino acid sequence for the protein
• The coding region always starts with the codon (AUG) and end with a stop codon.

The genetic code is universal and degenerate. Every living animal and plants (except a few) uses the exact same coding system. This pronounces the genetic code as universal. It is degenerate because there are a lot of codons which map to the same amino acid. This has no effect seen whatsoever.

3.5.4 Explain the process of translation, leading to polypeptide formation

Translation is the process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids in a polypeptide chain.

• Ribosomes bind to mRNA  in the cell's cytoplasm and move along the mRNA molecule in a 5' - 3' direction until it reaches a start codon (AUG)
• Anti-codons on tRNA molecules align opposite appropriate codons according to complementary base pairing 
• Each tRNA carries a specific amino acid
• Ribosome catalyse the formation of peptide bonds between adjacent amino acids (via a condensation reaction)
• The ribosome moves along the mRNA molecule synthesizing a polypeptide chain until it reaches a stop codon, at this point translation stops and the polypeptide chain is relesed

3.5.5 Discuss the relationship between one gene and one polypeptide

One gene is transcribed and translated to produce one polypeptide

A gene sequence is converted into a polypeptide sequence via the processes of transcription (making an mRNA transcript) and translation (polypeptide synthesis)

The universality of the genetic code means all organisms show the same relationship between genes and polypeptides (indicating a common ancestry and allowing for transgenic techniques to be employed)

The exceptions to this rules are:

• Genes that are encoding for tRNA and rRNA, aren't creating polypeptides.
• A single gene may code for multiple polypeptides if alternative splicing occurs.

Topic 3.4: DNA replication

3.4.1 Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of new complementary strands by DNA polymerase.

Helicase

• Unwinds the DNA and separates the two polynucleotides strands by breaking the hydrogen bonds between complementary base pairs.
• The two separated polynucleotide strands act as templates for the synthesis of new polynucleotide strands  

DNA polymerase

• Synthesis the new strands from the two parental template strands
• Free deoxynucleoside triphosphate are aligned opposite their complementary base partner and are covalently bonded together by DNA polymerase to form a complementary nucleotide chain.
• The energy for this reaction comes from the cleavage of the two extra phosphate groups 

3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequences of DNA

Each of the nitrogenous bases can only pair with its complementary pair.

• The significance of the mechanism outlined above is that the DNA molecule is copied precisely from one cell generation to the next
• The new strands formed will be identical to the original strands separated from the template
• The two DNA molecule formed will be identical to the original molecule

3.4.3 State that DNA replication is semi-conservative

DNA replication is a semi-conservative process because when a new strand of DNA is formed, one strand will be from the original DNA and one strand will be newly synthesized.

Topic 3.3: DNA structure

3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.

DNA Nucleotide

Deoxyribose is linked to the phosphate group with the 5th carbon and the 3rd carbon

Phosphate group is a phosphate with a negative charge

Nitrogenous Base could include (Adenine, Thymine, Cytosine and Guanine)


3.3.2 State the names of the four bases in DNA

In order with respect to the photo:

Adenine, Guanine, Thymine and Cytosine

Adenine and Guanine are both double ring nitrogenous bases (Purines)
Cytosine and Thymine are both single ring nitrogenous bases (Pyrimidines)


3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand.

Nucleotides are covalently bonded between the phosphate of one nucleotide to the C3 of the second nucleotide. The phosphate group creates a bridge connecting the C5 on one pentose and the C3 on the other. The bond is called the phosphodiester bond because it involves the phosphate group.


3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.

Two polynucleotides of DNA are held together by hydrogen bonds between complementary bases.

Guanine and Cytocine bonds together with a triple hydrogen bond (C=3)

Adenine and Thymine bonds together with a double hydrogen bond.

In order for the nucleotides to face each other, one strand is reversed to the other.


3.3.5 Draw and label a simple diagram of molecular structure of DNA

Topic 3.2: Carbohydrates, lipids and proteins

3.2.1 Distinguish between organic and inorganic compounds

Compounds containing carbon that are found in living organisms are called organic compounds.

The exceptions are the gas carbon dioxide, hydrogen carbonates and mineral calcium carbonate.

3.2.2 Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure.

3.2.3 List three examples each of monosaccharides, disaccharides and polysaccharides.

Monosaccharides

Glucose

Galactose

Fructose

Disaccharides

Lactose

Sucrose

Maltose

Polysaccharides

Glycogen

Starch

Cellulose

3.2.4 State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants.

Monosaccharides-
Glucose - (Animals and Plants) used for cellular respiration
Galactose - (Animals) Used for production of milk
Fructose - (Plants) Used in the production of sucrose

Disaccharides-
Lactose - (Animals) (Glucose + Galactose) Produced in mammary glands
Sucrose - (Plants) (Glucose + Fructose) Produced in green leaves
Maltose - (Plants) (Glucose + Glucose) Breakdown product in the hydrolysis of starch

Polysaccharides-
Glycogen - (Animals) Storage carbohydrates, stored in the liver and other cells
Starch - (Plants) Storage for carbohydrates
Cellulose - (Plants) Bundle of fibres as the main component of the cell walls.


3.2.5 Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides; between fatty acids, glycerol and triglycerides; and between amino acids and polypeptides.

Condensation Reaction: (Water is formed; similar to "condensation")

Hydrolysis Reaction: (Water is broken down; "lysis" refers to breaking down)

Monosaccharides forming a disaccharide: (Glycosidic Bond)

Fatty acids and Glycerol forming triglycerides: (Ester Bond)

Amino acids forming a polypeptide: (Peptide Bond)

3.2.6 State three functions of lipids

Structure: Phospholipids in the cell membrane allows for the cell to maintain its shape

Heat Insulation: A layer of fat under the skin to reduce heat loss

Buoyancy: Lipids are less dense than water, this allows animals to float

Energy Storage: Stores energy in the form of fat.

3.2.7 Compare the use of carbohydrates and lipids in energy storage.

Similarities:

• Complex carbohydrates (polysaccharides) and lipids both contain a lot of chemical energy and be used for energy storage
• Complex carbohydrates and lipids are both insoluble in water
• Carbohydrates and lipids both burn cleaner than proteins (They do not yield nitrogenous gas)

Differences:

• Lipids molecules contain more energy per gram than carbohydrates (2x)
• Carbohydrates are more readily digested than lipids and release their energy more rapidly
• Monosaccharides and disaccharides are water-soluble and easier to transport
• Animals tend to use carbohydrates primarily for short-term storage, while lipids are used more for long-term energy storage
• Carbohydrates are stored as glycogen in animals while lipids is stored in fat.